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V2.7

Version 2.7.0 (Dec 23, 2020)

Changes from version 2.6 which are relevant for users:

Changes leading to differences with previous versions

  • The definition of the omega angle has been modified to adhere to the IUPAC standard (i.e. with the previous amino acid)

New contributed modules:

  • A new Funnel module by Stefano Raniolo and Vittorio Limongelli
  • A new Infinite Switch Simulated Tempering in Force module by Glen Hocky
  • A new OPES module by Michele Invernizzi

New actions:

Other improvements:

  • MOLINFO action can now be used multiple times. Every action doing a search will use the latest appearance. See here.
  • Neighbor lists are now OpenMP and MPI parallel so improving the scalability of all actions employing them
  • It is now possible to pass pdb files with all weights set to zero. Instead of reporting an error, PLUMED will now assume they are all equal to 1/n, where n is the number of atoms (see here).
  • All the examples in the manual are now displayed with contextual help and regularly tested for correctness.
  • A tool to build PLUMED input directly within a python script has been added (see here and documentation for class plumed.InputBuilder()).
  • Python function plumed.read_as_pandas() now also accepts an argument index_col.
  • Lepton arithmetics can be used also when reading integers (e.g., METAD PACE=2*5, see here).

GROMACS:

  • When using -hrex flag, the neighbor lists are update automatically at every exchange step. This relaxes the requirements on the choice of -replex stride (see here, thanks to Chang Junhan).

Changes in the DRR module

  • Support multi-time stepping. Now the STRIDE keyword should work with DRR correctly.
  • Support reflecting boundary conditions, which should be a better solution to the boundary effect of eABF in non-periodic cases. You can use REFLECTINGWALL to enable it.
  • Stop the simulation when the temperature is not passed from the MD engine to PLUMED. In this case, users should set the temperature by the TEMP keyword.

Changes in the ISDB module

  • There is a new option for OPTSIGMAMEAN, SEM_MAX that allows to automatically determine an optimal value for SIGMA_MAX

Changes in the VES module

  • Small changes to TD_MULTICANONICAL and TD_MULTITHERMAL_MULTIBARIC. Bug fix concerning the calculation of the logarithm of the target distribution. Added the keyword EPSILON to avoid dealing with regions of zero target probability.

For developers:

  • small fix in Plumed.h too avoid unique global symbols (see here)
  • Added cmd("readInputLines") to allow reading input from a buffer with comments and continuation lines (see here).
  • fixed error when the install prefix contained unicode characters

Version 2.7.1 (Apr 16, 2021)

  • Includes all fixes up to 2.6.3
  • In python interface, fixed usage of python arrays to allow compatibility with PyPy.
  • New/updated patches:
  • updated patch for gromacs-2020.5
  • new patch for gromacs-2021
    • this should work with multiple-time stepping (plumed forces are integrated with the smallest time step, plumed can internally implement a multiple-time step if needed).
    • Modular simulator is still not supported
    • hrex, lambda cv and replica-exchange are not yet tested

Version 2.7.2 (Jul 27, 2021)

  • Includes all fixes up to 2.6.4
  • Fixed a bug in the -hrex implementation for GROMACS 2020 and 2021 (see #691, thanks to Chang Junhan).
  • Changes in the OPES module
  • the CALC_WORK option now outputs the accumulated work, as in METAD, instead of the work done in the last bias update

Version 2.7.3 (Dec 1, 2021)

  • Includes all fixes up to 2.6.5
  • GROMACS patches now take a note of the used PLUMED version in the GROMACS log (see here)
  • GROMACS 2021 patch renamed to 2021.4 for consistency.

Version 2.7.4 (Feb 22, 2022)

  • Includes all fixes up to 2.6.6

Version 2.7.5 (Oct 21, 2022)

  • Minor fixes in error reporting.
  • Fix in building python package with MacPorts and MacOS 11.
  • Fixed overflows when using plumed sum_hills --idw, see here.
  • Renamed version file to VERSION.txt to avoid issues with some MacOS compilers.
  • Fixed periodicity bug in pesmd.
  • Fixed an issue with timestep roundoff apparent in Windows build.
  • Fixed an issue with METAINFERENCE noisetype OUTLIERS/MOUTLIERS when not using replicas, thanks @hmcezar #847
  • Fixed this problem.
  • Fixed this problem.
  • Fixed an incorrect const conversion in wrapper/Plumed.h.

Version 2.7.6 (Mar 13, 2023)

Not maintained

This branch is not maintained Users are invited to upgrade to a newer version.

  • Fixed a bug in pathtools where the distance was not squared and the suggested lambda was incorrect, thanks @rebelot #894
  • Fixed a bug in SAXS cv using recent versions of arrayfire
  • Fixed checks on the number of used CVs in TD_MULTICANONICAL and TD_MULTITHERMAL_MULTIBARIC
  • Fixed PIV with VOLUME, see here.
  • Fixed generation of documentation with MPI examples.
  • plumed patch properly detects code patched with --include option (available as of plumed 2.9, might become the default)